I recommend flying. When you arrive in SJU you won't have to do customs/immigration. As you say, you will need to collect your bags and recheck them but it's easy and you have plenty of time. No test or portal required for in-transit passengers in SJU Just show the national guard your IC flight information and they will direct you up to the ticket counters to check your bags. There is a great wine bar at the beginning of B concourse that is easy to kill time at and they have great Puerto Rican food.

I prefer to fly for a couple of reasons. No USVI portal to deal with, the arrival is much more organized and efficient at the airport, if there is a flight issue you have options but no options with the ferry, I'd rather get stuck in San Juan than St Thomas.